|
| Status |
Public on Apr 05, 2012 |
| Title |
Digital Genomic Footprinting assay of H1 BMP4 Derived Mesendoderm Cultured Cells; DGF.DS19310 |
| Sample type |
SRA |
| |
|
| Source name |
Human embryonic stem cells received from the James Thomson laboratory. Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; DGF.DS19310
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: BMP4-03
sample common name: H1 BMP4 Derived Mesendoderm Cultured Cells
molecule: genomic DNA
disease: None
biomaterial_provider: James Thomson Laboratory
biomaterial_type: Cell Line
line: H1
lineage: Embryonic Stem Cell
differentiation_stage: Embryonic stem cell differentiated into mesendoderm by treatment with BMP4
differentiation_method: H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days
passage: Between 20 and 30
medium: E8
Sex: Male
batch: BMP4-3
experiment_type: Digital Genomic Footprinting
extraction_protocol: Qiagen minElut
dnase_protocol: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction protocol: Single read - Illumina
|
| |
|
| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
sample_term_id: NTR_0000856
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS19310
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12039
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7805
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
|
| Data processing |
**********************************************************************
ANALYSIS FILE NAME: GSM909313_UW.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Digital_Genomic_Footprinting.DGF.DS19310.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS19310.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on the H1 BMP4 Derived Mesendoderm Cultured Cells, Library DGF.DS19310 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13110
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 8
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 323,679,569
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.4331
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.4824
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5191
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM909313_UW.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Digital_Genomic_Footprinting.DGF.DS19310.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS19310.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library DGF.DS19310 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13115
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HBDM DGF 10
BROWSER_TRACK_DESCRIPTION: UW H1 BMP4 Derived Mesendoderm Cultured Cells Digital Genomic Footprinting Library DGF.DS19310 EA Release 8
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 323,679,569
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.4331
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.4824
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5191
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
|
| |
|
| Submission date |
Apr 04, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Northwest REMC |
| E-mail(s) |
rharris1@bcm.tmc.edu
|
| Organization name |
University of Washington
|
| Street address |
-
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
|
| Relations |
| SRA |
SRX135565 |
| BioSample |
SAMN00631730 |
| Named Annotation |
GSM909313_UW.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Digital_Genomic_Footprinting.DGF.DS19310.wig.gz |
